Advances in oncology research have led to the development of personalized treatments based on specific knowledge of a patient’s tumor. New therapies have been customized to target signaling pathways that are hyperactivated or block specific variants of cell surface molecules, thus leading to better anti-tumor responses. Next generation sequencing (NGS) technology has been at the forefront of these breakthroughs by enabling researchers to rapidly sequence RNA transcripts (RNA-seq) or exons (whole exome sequencing; WES) within tumor tissue and translate these findings into novel therapies.
Consider these key features of RNA-seq and WES as you develop experiments with animal models or evaluate preclinical or clinical samples.
RNA-seq: This NGS technology is now considered the gold standard of RNA analysis as it can sequence large numbers of transcripts at the tissue or single cell level and can measure differential gene expression, compare changes in transcripts between untreated and treated groups, and detect fusion transcripts caused by chromosomal rearrangements, which are a hallmark of a variety of tumor types. RNA-seq analysis is used routinely in preclinical animal models, especially for comparisons between Standard-of-Care and experimental treatments.
WES: The measurement of tumor mutation load (TML) in a biopsy is critical for evaluating the efficacy of immunotherapies and developing new targeted approaches. WES has become a widely accepted approach for measuring TML in both liquid and solid tissue biopsies as this method can detect mutations in regions of the genome that encode proteins. This approach is faster than whole genome sequences and can identify genetic variants or changes in copy number contributing to TML and can also be used for HLA typing, which inform the selection of different therapeutic approaches.
Consider working with experts in NGS technology to advance your preclinical and clinical oncology research. Their expertise will maximize the benefit of using such approaches in your research and advancing the development of new oncology treatments.